Gary M. Troup

Y chromosome polymorphisms in native American and Siberian populations: identification of native American Y chromosome haplotypes.

Abstract We have initiated a study of ancient male migrations from Siberia to the Americas using Y chromosome polymorphisms. The first polymorphism examined, a C→T transition at nucleotide position 181 of the DYS199 locus, was previously reported only in Native American populations. To investigate the origin of this DYS199 polymorphism, we screened Y chromosomes from a number of Siberian, Asian, and Native American populations for this and other markers. This survey detected the T allele in all five Native American populations studied at an average frequency of 61%, and in two of nine native Siberian populations, the Siberian Eskimo (21%) and the Chukchi (17%). This finding suggested that the DYS199 T allele may have originated in Beringia and was then spread throughout the New World by the founding populations of the major subgroups of modern Native Americans. We further characterized Native American Y chromosome variation by analyzing two additional Y chromosome polymorphisms, the DYS287 Y Alu polymorphic (YAP) element insertion and a YAP-associated A→G transition at DYS271, both commonly found in Africans. We found neither African allele associated with the DYS199 T allele in any of the Native American or native Siberian populations. However, we did find DYS287 YAP+ individuals who harbored the DYS199 C allele in one Native American population, the Mixe, and in one Asian group, the Tibetans. A correlation of these Y chromosome alleles in Native Americans with those of the DYS1 locus, as detected by the p49a/p49f (p49a,f) probes on TaqI-digested genomic DNA, revealed a complete association of DYS1 alleles (p49a,f haplotypes) 13, 18, 66, 67 and 69 with the DYS199 T allele, while DYS1 alleles 8 and 63 were associated with both the DYS199 C and T allele.

Strategies for unambiguous detection of allelic heterozygosity via direct dna sequencing of PCR products: Application to the hla drb1 locus

Background: Many genetic loci exhibit substantial heterogeneity: the human leukocyte antigen (HLA) DRB loci include 139 alleles and the cystic fibrosis transmembrane regulator gene more than 500 known mutations. Identification of alleles at these loci is cumbersome with typical molecular diagnostic methods such as hybridization assays or restriction enzyme analysis. Direct DNA sequencing of polymerase chain reaction (PCR) products is a general approach to complex loci that allows detection of any allele within the nucleotide sequence analyzed. However, direct DNA sequence-based unambiguous identification of heterozygous nucleotide positions using PCR templates is a challenging problem. Methods and Results: The ability of direct DNA sequencing methods to accurately identify HLA DRB alleles was assessed. The authors evaluated the performance of modified T7 and Taq DNA polymerases in isothermal and thermal cycle sequencing of PCR products derived from HLA DRB genes in 235 individuals who were potential donors or recipients of bone marrow transplants. The uniformity of peak intensity and ability to identify heterozygous nucleotide positions was similar when either AmpliTaq FS- or Sequenase DNA polymerase-derived electropherograms were prepared. The modified Taq DNA polymerase allowed the use of unpurified, double-stranded PCR templates. Furthermore, this enzyme could be used in less laborious, less costly cycle sequencing assays coupled with automated fluorescent detection methodology. Direct sequencing performed with either enzyme allowed unambiguous identification of DRB1 alleles, resolution of difficult heterozygous combinations, and recognition of new alleles. Conclusions: The direct DNA sequencing methods employed here for HLA allele identification are relatively efficient and semiautomated, and may be reasonably considered as a general approach to other complex molecular diagnostic problems, especially when coupled to simplified sequencing chemistries allowing cycle sequencing.

Studies on the relationship between HLA DR4 and in vitro IgM rheumatoid factor production

The relationship between the presence of the DR4 antigen and other HLA antigens and in vitro production of IgM-rheumatoid factor by lymphocytes from a group of healthy young subjects was examined. Pokeweed and Epstein--Barr virus-stimulated lymphocyte cultures were examined for the production of rheumatoid factor and immunoglobulins. No significant correlation was found between the presence of the DR4 antigen and in vitro production of IgM rheumatoid factor. The presence of the B18 antigen seemed to identify a population of nonresponders when stimulated with PWM.

A new DRB1 allele (DRB1*0811) identified in Native Americans

A novel DRB1 allele was identified in a potential bone marrow transplantation recipient and her father. Both are Native Americans of Navajo descent. Class II serologic typing of the patient demonstrated the presence of DR8, DR14, DR52, and DQ3. Sequence specific polymerase chain reaction (PCR) amplification of genomic DNA was consistent with the DRB1 alleles *08 and *14. Direct DNA sequencing of PCR products prepared from genomic DNA demonstrated that the patient`s class II alleles included the novel allele, DRB1*1402, DRB3*0101, DQB1*0301, and DQB1*0402. Analysis of the siblings and the father of this individual revealed that the new allele was transmitted on the haplotype A2, Cw7, B39, DQB1*0402, while the DRB1*1402 allele was transmitted on the haplotype A24, Cw4, B35, DRB3*0101, DQB1*0301. 4 refs., 1 fig., 1 tab.

Anti-idiotypic antibodies to anti-DR in patients with rheumatoid arthritis.

Rheumatoid arthritis (RA) sera were evaluated for anti-idiotypic (anti-id) antibodies to HLA-DR antigens (anti-DR) using an ELISA method with murine monoclonal anti-DR antibody-coated microtiter plates incubated serially with either normal or RA sera and peroxidase-conjugated goat anti-human IgG (Fc specific). Specificity was examined using other monoclonal antibodies including anti-Leu 3a, OKM5, OKT8, anti-cytochrome c, and anti-breast tumor antigen. Significant binding of 11/33 (33%) RA to anti-DR was found compared with 0/44 normals (P less than 0.001). Two groups were identified: RA sera reacting with anti-DR and anti-Leu 3a and sera which did not bind to anti-DR but bound to irrelevant monoclonal antibodies. Anti-DR reactivity was differentiated from anti-Leu 3a by competitive inhibition studies. Binding of whole sera and IgG from RA patients to anti-DR was significantly inhibited by DR+ cell extract. The same extract was not inhibitory after selective removal of DR antigen by adsorption on an anti-DR-Sepharose column. These data suggest that anti-id antibodies are directed against the antigen-binding site of id. We conclude that some RA patients have anti-id antibodies potentially involved in immunoregulation of anti-DR antibodies.